Contacts of the helix formed by residues 376 - 387 (chain C) in PDB entry 1D2V
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 376 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205C ASP* 3.5 19.7 - - - -
345C ARG* 6.0 0.2 - - - -
370C ARG 5.0 0.3 - - - +
371C VAL* 3.1 29.3 + - - +
372C VAL 5.2 1.2 + - - -
374C GLU 3.6 3.6 - - - +
375C GLY* 1.3 80.7 - - - +
377C ILE* 1.3 63.4 + - - -
379C PRO* 3.7 4.7 - - - +
380C ILE* 3.6 19.0 - - - +
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Residues in contact with ILE 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C ASP* 2.9 24.4 + - - +
210C LEU* 4.8 0.7 - - + -
248C SER* 3.4 41.5 - - - +
251C THR* 4.0 20.4 - - + +
252C LEU* 4.4 4.5 - - - +
255C ARG* 3.2 33.0 - - - +
371C VAL* 4.2 17.5 - - + -
376C GLY* 1.3 75.9 - - - -
378C ASP* 1.3 64.0 + - - +
379C PRO 3.6 0.4 - - - -
380C ILE* 3.4 3.3 + - - +
381C LEU* 2.9 48.2 + - + +
541C THR* 4.2 5.4 - - + -
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Residues in contact with ASP 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C ASP* 4.7 3.5 - - - +
206C ASN* 4.7 14.9 + - - +
208C ARG* 5.2 1.0 + - - -
255C ARG* 4.7 1.2 + - - -
375C GLY 4.4 2.2 + - - +
376C GLY 3.6 0.4 - - - -
377C ILE* 1.3 82.3 - - - +
379C PRO* 1.4 65.4 - - + +
381C LEU* 3.3 1.1 + - - -
382C ARG* 2.9 47.4 + - - +
541C THR* 3.3 22.0 - - - +
542C GLY* 3.1 30.5 + - - -
543C ILE* 3.6 19.1 - - + +
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Residues in contact with PRO 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C ARG* 3.5 16.1 - - + -
346C LEU 3.1 35.7 + - - +
347C ASP* 5.7 0.4 - - - -
353C MET* 3.4 32.3 - - - -
374C GLU 5.1 0.2 - - - +
375C GLY* 3.3 24.0 - - - +
376C GLY 3.7 4.5 - - - +
377C ILE 3.6 1.1 - - - -
378C ASP* 1.4 93.2 - - + +
380C ILE* 1.4 55.5 + - - +
382C ARG* 3.6 7.5 + - - +
383C GLY 2.9 22.9 + - - -
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Residues in contact with ILE 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C PRO* 3.8 24.0 - - + +
245C GLU* 3.6 32.5 - - + +
248C SER* 3.1 34.5 - - - +
343C MET* 4.4 9.4 - - + -
344C PHE 4.1 7.5 - - - +
345C ARG* 4.2 18.8 - - + +
370C ARG 5.4 2.0 - - - +
371C VAL* 4.4 13.2 - - + +
376C GLY 3.6 19.1 - - - +
377C ILE* 3.4 3.6 + - - +
378C ASP 3.2 0.2 - - - -
379C PRO* 1.4 74.8 - - - +
381C LEU* 1.3 59.2 + - - +
383C GLY* 3.1 3.1 + - - -
384C LEU* 2.9 29.3 + - + +
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Residues in contact with LEU 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A MET* 4.2 9.7 - - + +
248C SER* 3.9 20.4 - - - +
249C MET* 3.7 31.0 - - - -
252C LEU* 4.7 7.0 - - + -
377C ILE* 2.9 34.1 + - + +
380C ILE* 1.3 74.7 - - - +
382C ARG* 1.4 64.1 + - - +
384C LEU* 3.3 9.0 + - + +
385C MET* 3.1 33.9 + - + +
537C ILE* 4.4 14.1 - - + -
541C THR* 3.9 28.3 - - + -
543C ILE* 3.8 13.7 - - + -
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Residues in contact with ARG 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758A BR 3.5 17.2 - - - +
346C LEU* 3.1 24.4 + - + -
347C ASP* 2.7 33.4 + - - +
348C ASN* 3.2 20.8 - - - +
350C TYR* 3.3 54.2 - - + +
378C ASP* 2.9 26.4 + - - +
379C PRO* 3.8 20.0 - - - +
381C LEU* 1.4 72.4 - - - +
383C GLY* 1.3 66.3 + - - +
385C MET* 3.1 2.7 + - - +
386C ALA* 2.9 23.2 + - - +
542C GLY 5.0 1.6 + - - -
543C ILE* 3.9 23.0 - - + +
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Residues in contact with GLY 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 4.6 1.7 - - - +
344C PHE* 3.2 32.3 - - - -
346C LEU* 3.9 13.0 - - - +
379C PRO 2.9 12.0 + - - -
380C ILE 3.1 0.8 + - - -
382C ARG* 1.3 78.2 - - - +
384C LEU* 1.3 62.0 + - - +
387C THR* 2.9 29.4 + - - -
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Residues in contact with LEU 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A SER* 3.7 0.7 - - - -
84A LEU* 3.3 40.6 + - + +
85A MET* 3.0 46.2 + - + +
87A MET* 4.9 0.7 - - + -
88A GLN* 3.8 36.1 - - + +
245C GLU* 3.9 37.9 - - + +
249C MET* 4.5 0.4 - - - -
380C ILE* 2.9 17.6 + - + +
381C LEU* 3.6 18.2 - - + +
382C ARG 3.3 0.2 - - - -
383C GLY* 1.3 78.4 - - - +
385C MET* 1.3 60.3 + - - +
387C THR 3.7 0.3 - - - +
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Residues in contact with MET 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A SER* 3.9 3.5 - - - -
85A MET* 4.4 8.1 - - + -
350C TYR* 3.5 19.1 - - - +
381C LEU 3.1 30.2 + - - +
382C ARG 3.1 3.8 + - - +
384C LEU* 1.3 78.2 - - - +
386C ALA* 1.3 57.4 + - - +
387C THR 3.5 0.4 - - - -
534C PRO* 5.6 0.2 - - - -
537C ILE* 3.9 37.7 - - + -
543C ILE* 4.1 6.7 - - + -
546C VAL* 4.1 10.5 - - + -
547C SER* 3.0 40.1 + - - +
551C ILE* 4.1 16.6 - - + -
554C SER 3.6 7.4 - - - +
555C ASN* 3.3 21.1 - - - -
561C PHE* 3.7 12.9 - - + -
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Residues in contact with ALA 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346C LEU* 3.7 10.0 - - + +
350C TYR* 3.5 33.4 - - + -
382C ARG 2.9 8.5 + - - +
385C MET* 1.3 75.5 - - - +
387C THR* 1.3 62.1 + - - +
388C PRO* 4.5 0.7 - - - +
555C ASN 3.1 17.6 - - - +
556C SER* 4.9 1.2 - - - -
557C TYR* 4.2 12.4 + - + +
561C PHE* 3.8 10.3 - - + -
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Residues in contact with THR 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A SER* 3.5 3.5 - - - -
84A LEU* 2.7 36.5 + - + +
340C GLN* 4.4 2.9 - - - +
344C PHE* 3.6 54.4 - - + +
346C LEU* 4.8 3.8 - - - +
383C GLY* 2.9 19.8 + - - -
384C LEU 3.7 0.9 - - - +
385C MET 3.5 0.4 - - - -
386C ALA* 1.3 81.0 + - - +
388C PRO* 1.4 74.4 - - + +
555C ASN* 4.2 2.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il